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- PDB-1s5v: Crystal Structure Analysis of a mutant of DIHYDRODIPICOLINATE SYN... -

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Basic information

Entry
Database: PDB / ID: 1s5v
TitleCrystal Structure Analysis of a mutant of DIHYDRODIPICOLINATE SYNTHASE--residue Tyr107 to Phe107
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / SYNTHASE / DIHYDRODIPICOLINATE
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / identical protein binding / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel ...4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDobson, R.C.J. / Valegard, K. / Gerrard, J.A.
CitationJournal: J.MOL.BIOL. / Year: 2004
Title: The Crystal Structure of Three Site-directed Mutants of Escherichia coli Dihydrodipicolinate Synthase: Further Evidence for a Catalytic Triad
Authors: Dobson, R.C.J. / Valegard, K. / Gerrard, J.A.
History
DepositionJan 21, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)62,5782
Polymers62,5782
Non-polymers00
Water4,161231
1
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase

A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)125,1564
Polymers125,1564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
2
A: Dihydrodipicolinate synthase

B: Dihydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)62,5782
Polymers62,5782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
Buried area2580 Å2
ΔGint-20 kcal/mol
Surface area20970 Å2
MethodPISA
3
A: Dihydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)31,2891
Polymers31,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: Dihydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)31,2891
Polymers31,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)120.888, 120.888, 110.202
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Dihydrodipicolinate synthase / DHDPS


Mass: 31288.936 Da / Num. of mol.: 2 / Mutation: Y107F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DAPA / Plasmid: pRD002 / Production host: Escherichia coli (E. coli) / Strain (production host): AT997 / References: UniProt: P0A6L2, dihydrodipicolinate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 10
Details: potassium phosphate (0.0012ml, 1.8M, pH10), N-octyl-beta-R-glucopyrandoside (0.0006ml, 6% w/v), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 38813 / % possible obs: 98.6 % / Rmerge(I) obs: 0.114
Reflection shellResolution: 2.35→2.41 Å / Rmerge(I) obs: 0.28 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DHP

1dhp


Resolution: 2.35→20.94 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.396 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23174 1942 5 %RANDOM
Rwork0.19523 ---
all0.19705 ---
obs0.19705 36809 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.689 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å2-0.65 Å20 Å2
2---1.3 Å20 Å2
3---1.95 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4317 0 0 231 4548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214386
X-RAY DIFFRACTIONr_bond_other_d0.0020.024112
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9595965
X-RAY DIFFRACTIONr_angle_other_deg0.87139524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9985582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024916
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02810
X-RAY DIFFRACTIONr_nbd_refined0.1980.21602
X-RAY DIFFRACTIONr_nbd_other0.2350.24872
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1520.23779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.271
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.2138
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4641.52896
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88224660
X-RAY DIFFRACTIONr_scbond_it1.32331490
X-RAY DIFFRACTIONr_scangle_it2.3634.51305
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.246 162
Rwork0.211 2633

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